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Hisat2 computing efficiency too low

I use wsl(ubuntu) to run Hisat2, it covers >30% cpu and >=0.1 memory while cpu and memory went very high at the time I use hisat2-build how can I improve the computing efficiency？ thanks！

hisat2 rnaseq
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written by ianlee96 • ianlee96

this is the script I use

 #!/bin/bash
    for i in {LbG1,LbG2,LbG3,LbT1,LbT2,LbT3,LbR1,LbR2,LbR3,LrG1,LrG2,LrG3,LrT1,LrT2,LrT3,LrR1,LrR2,LrR3}
    do echo $i
        hisat2 -x index_build -1 /mnt/c/SCIProgram/trans/01clean_data/${i}_1.clean.gz -2 /mnt/c/SCIProgram/trans/01clean_data/${i}_2.clean.gz -S /mnt/c/SCIProgram/trans/02hisat2/hisat2_output/${i}_hisat2_output -p 11
    done

and this is the code

bash run.sh
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written by ianlee96 • ianlee96

What machine are you running on, how many cores and memory total, and is this SSD or spinning disks?

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written by ATpoint ATpoint

6cores, 12 threads, 8 mem, ssd, windows11(wsl/Ubuntu)

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written by ianlee96 • ianlee96

1 answer

I solved the problem by rebuilding index

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written by ianlee96 • ianlee96

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